Biological Physics FYS4715 2020 Some questions Write, 5 min, read aloud the parts you want, publish anonymously, helpful for me • Why did you choose to follow FYS4715? • What do you expect to get out of the course? • What have you learnt previously that is relevant for the course? • What education background do you have? Themes this year • General: Processes on cellular and molecular scale • 1nm – 100 um • from atomic to macroscopic: stat mech • small scale: atomic forces, velocities, charges • large scale: surface tension, stress-strain, diffusion, osmosis, electrochemistry • Nelson ch 1-8, 12 + chosen topics • Projects: • Passive and active swimmers • Cellular Potts model (?) • Mechanobiology, effects of ultrasound on cells • Bioimpedance • Nerve impulses Chapter 1 • What is heat? • Entropy • 2nd law vs. order • Free energy • Osmosis • Physical models • For biologists: https://www.natur e.com/articles/d41 586-019-03960-z Biological Physics • In physics we make mathematical models and calculate stuff • What is the volume of one molecule of water? • Most famous model: ideal gas • equation of state: PV = nkBT • What is PV? • How much is kBT? pN forces nm distances Chapter 2: What’s inside cells • Biological question: How do organisms organize all the chemical processes? • Physical ideas • Compartmentalization • Active transport • Specific processes • Non-linearity -> switching in networks Polar – hydrophilic – water soluble Hydrophobe & amphiphile higher energy cost energy and entropy Important molecules • Important nitrogenous bases: Adenine, Thymine, Guanine, Cytesine, Uracil • Nucleic acids • DNA (DeoxyriboNucleic Acid): base pairs T-A, C-G • RNA (RiboNucleic Acid): single strands of G,U,A,C • Nucleotide = (nitrogenous) base + sugar + phosphate • Adenine (base) + ribose (sugar) = Adenosine • ATP (Adenosine TriPhosphate) • ADP (Adenosine DiPhosphate) energy in energy out Important molecules • fatty acids -> phospholipid -> membranes • amino acids -> polypeptides - proteins Amino: NH2, Acid: OOH Peptides: 2-50 amino acids Proteins: >50 amino acids Molecule databases • https://www.rcsb.org protein data bank • 1aoi • 1tau • 1mbn • Proteins are folded • info on different scales • https://www.ucalgary.ca/tieleman/ • atomify Cells – fundamental functional units of life • enclosed by plasma membrane • interior «soup» called cytoplasm • organized in organelles = specialized compartments surrounded by membrane • nucleus: contains the genetic information necessary for cell growth and reproduction • mitochondria: responsible for the energy transactions necessary for cell survival • lysosomes: digest unwanted materials within the cell • endoplasmic reticulum & Golgi apparatus: organization of the cell by synthesizing selected molecules and then processing, sorting, and directing them to their proper locations cyto- = cell Plasma membrane Cytosceleton - actin filaments (7 nm Ø) - microtubules (25 nm Ø) - intermediate filaments (10 Ø) The euKaryotic cytosKeleton. Actin filaments are shown in red, and microtubules composed of beta tubulin are in green. physics questions: G-actin monomer • polarization F-actin polymer • force Crash course in greek and latin: Angio- Vessel -atomy, -otomy cutting Angiogenesis Auto- self =production Brachy short of vessels Cata- (katalysis) dissolving Carcino- tumor (crab-like) Centro-, -centric centre Carcinogenesis -ceptor, ceptive capere, to take = Chromo- color Production Chrono- time (development)o -cyte, cyto- hollow f cancer Diplo double e-, ec- out of Endo- within, inside Exo- outside Extra- beyond Erythro- red -gen, genous descent -genic, -genous birth, descent, origin -genic, -genous to produce Crash course in greek and latin: Glia- glue Haem- blood Histo- tissue Homeo- alike Homo- the same Hyper- above Hypo- under Infero- beneath Infra- below Inter- between Intra- within Iso- equal -kinesis, -kinetic kinesis=movement Leuko- white Lipo- fat -lysis, -lysin dissolving Macro- large Medi- middle Crash course in greek and latin: -mere, mero- a part Meta- after Metabolism change Centromere= Micro- small middle part Mito- (mitosis) a tread Mono- single Muta- mutare=to change telomere= Necro- dead end part Neuro- nerve -nomics law Oligo- few Onco- bulk, mass Ortho- straight Para- beside Per- through Peri- around -phage, -phagous phagein=to eat -phil to love Crash course in greek and latin: -phobe to fear Photo- light Plasma-, -plasm form -plicate to fold Post- after Pre- before Pro- before Proto- first Re- back Retro- backwards Serum whey (myse) -some, soma- body Stereo-, -steric solid Sub- under Super- over Supra- above Sym-, syn- with Crash course in greek and latin: -synthesis composition Tauto- the same Tele- far Teleo- complete Telo-, telio- end Trans- across Ultra- beyond Statistical mechanics • Model: MD (Atomify) 23 2 • micro xi, mi, vi, fij, 10 -> macro r, <v>, <v >, Ek, • thermodynamics: P, T, cP,Hv,... (stat + conservation laws) • distributions: uniform, Gaussian, Poisson "!" " 1 ! ! � � = � #$" � 2� • x->vx, x0->0, s • <v>, <v2> • Model: ideal gas.